Rapid and efficient capture of dna from sample without using cell lysing reagent

ABSTRACT

Nucleic acids can be made available for amplification or other treatment after admixture of a sample with specific weakly basic polymers to form a precipitate with the nucleic acids at acidic pH. After removing non-precipitated materials, the pH is then made basic, thereby releasing the nucleic acids from the polymer. This method for preparing specimen samples is simple and quite rapid, and the released nucleic acids can be further treated in hybridization assays or amplification procedures. No surfactant or other cell lysing reagents are employed. The weakly basic polymers are water-soluble and cationic at acidic pH, but neutral in charge at basic pH.

CROSS REFERENCE TO RELATED APPLICATIONS

This application claims priority from U.S. Provisional Application60/132,443, filed May 4, 1999, and Non-Provisional application U.S. Ser.No. 10/019,514 filed Feb. 21, 2003 under U.S. Pat. No. 7,262,006, andDivisional application U.S. Ser. No. 11/613,475 filed Dec. 20, 2006,which is incorporated by reference in its entirety.

FIELD OF THE INVENTION

This invention relates to a method for preparing a sample by capture andselective release of nucleic acids for detection. In particular, itrelates to a method for capture and release of nucleic acids forsubsequent treatment such as amplification. It also relates to a testkit for use in the method.

BACKGROUND OF THE INVENTION

Technology to detect minute quantities of nucleic acids has advancedrapidly over the last two decades including the development of highlysophisticated amplification techniques such as polymerase chain reaction(PCR). Researchers have readily recognized the value of such technologyto detect nucleic acids which are indicative of diseases and geneticfeatures in human or animal test specimens. The use of probes andprimers in such technology is based upon the concept of complementarity,that is, the bonding of two strands of a nucleic acid by hydrogen bondsbetween complementary nucleotides (also known as nucleotide pairs). PCRis a significant advance in the art to allow detection of very smallconcentrations of a targeted nucleic acid. The details of PCR aredescribed, for example, in U.S. Pat. No. 4,683,195 (Mullis et al), U.S.Pat. No. 4,683,202 (Mullis) and U.S. Pat. No. 4,965,188 (Mullis et al),although there is a rapidly expanding volume of literature in thisfield.

In order to effectively amplify and detect a target nucleic acid, it isusually necessary to isolate that nucleic acid from cellular and otherspecimen debris. Various lysing procedures are known, includingfreezing, treatment with digesting enzyme such as proteases (forexample, Proteinase K), boiling, and use of various detergents (see forexample U.S. Ser. No. 178,202, filed Apr. 6, 1988 by Higuchi, and EP-A-0428 197, published May 22, 1991), solvent precipitations and heatingprotocols.

Circulating DNA has been detected in blood serum and plasma. Nanogramquantities are detected in normal subjects (Steinman, C. R., J. Clin.Invest. 56:512-515, 1975 and Raptis, L., et al., J. Clin. Invest.66:1391-1399, 1980), and increased levels are detected in chronicautoimmune diseases (Leon, S. A., et al., Cancer Res., 37:646-650, 1977)and in cancer patients (Stroun, M., et al., Eur. J. Cancer Clin. Oncol.28:707-712, 1987; Maebo, A., Jpn. J. Thorac. Dis. 28:1085-1091, 1990;Fournie, G. J., et al., Cancer Lett., 91:221-227, 1995; Lin, A., et al.,BioTechniques 24:(6) 937-940, 1998; and Sorenson, G. D., et al., CancerEpidemiology, Biomarkers and Prevention 3:67-71, 1994). Recently, it hasbecome evident that free extracellular DNA present in blood serum andplasma can be used for genotype analysis (Lin, A., et al., BioTechniques24:(6) 937-940, 1998), for detection of cancer (Mulcahy, H. E., et al.,Clin. Cancer Res. 4:271-275, 1998), and DNA in maternal serum may beused in prenatal diagnostics (Lo Dennis, et al., Am. J. Human Genet.62:768-775, 1998). Mutations present in a primary tumor, often can bedetected using DNA from blood plasma or serum DNA (Sorenson, G. D., etal., Cancer Epidemiology, Biomarkers and Prevention 3:67-71, 1994;Vasyukhin, V., et al., In Challenges of Modern Medicine, Vol. 5,Biotechnology Today, R. Verna, and A. Shamoo, eds, 141-150. Aera-SeronoSymposia Publications, Rome; Mulcahy, H. E., et al., supra.; Kopreski,M. S., et al., Brit. J. Cancer 76:1293-1299, 1997; Chen, X., et al.Nature Medicine 2: 1033-1035, 1996; Vasioukin, V., et al., Brit. J.Haematology 86:774-779, 1994; and Tada, M., et al., Cancer Res.53:2472-2474, 1993). Thus, DNA present in serum and plasma represents aminimally invasive source for information related to cancer diagnosis,prognosis, and therapy.

To effectively amplify and detect a target nucleic acid, it is usuallynecessary to separate the nucleic acid from interfering substancespresent in a specimen of interest. Several different approaches havebeen used to concentrate and purify DNA from blood serum or plasma. Manyof these methods involve multiple steps including phenol, ether, andchloroform treatment, dialysis, passage through Concanavalin A-Sepharoseto remove polysaccharides and then centrifugation in a cesium chloridegradient (Vasyukhin, V., et al., supra.). More recently, Qiagen hascommercialized a system for DNA concentration and purification based ona spin column protocol. The Quiagen protocol is complex, involving atotal of eight steps, treatment with a protease, incubations at 70° C.,and requires the use of at least 3 different buffers, in addition to asilica spin column centrifugation step.

Recently, Goecke et al.(WO 97/34015)reported the detection ofextracellular tumor-associated nucleic acid in blood plasma and serumusing nucleic acid amplification assays. In their preferred method, DNAis co-precipitated from plasma and serum using a multistep protocolinvolving an initial co-precipitation by gelatin, followed by solventtreatment and centrifugation. Other time-consuming and complex protocolsinvolving the use of glass beads, silica particles or diatomaceous earthfor extraction of DNA from serum and plasma are also described.

The use of weakly basic polymers for the capture and selective releaseof nucleic acids has been described U.S. Pat. No. 5,622,822 (Ekeze etal.), U.S. Pat. No. 5,582,988 (Backus et al.), and U.S. Pat. No.5,434,270 (Ponticello, et al.). The protocols described in theaforementioned patents depend upon the use of a cell lysing agent or acell lysing step. Surfactants are often used as cell lysing agents.

The use of surfactants and other lysing agents results in the release ofnucleic acids from cells and cellular components in blood; causing alarge concentration of background DNA.

SUMMARY OF THE INVENTION

The problems associated with the use of lysing agents or lysing steps inprior art methods have been overcome with the method of the presentinvention.

The method of this invention involves the use of a weakly basic polymer,as described in the above-indicated US patents, for the capture andselective release of the captured nucleic acids from the polymer, butwithout the use of a lysing step or lysing agent, as performed usingprior art methods.

According to one aspect of the invention, a simplified, easy-to-usemethod for recovering DNA from blood serum and plasma is provided. Themethod includes the use of a weakly basic polymer for binding DNA from asample such as blood serum or plasma. Upon binding DNA, the polymerbecomes insoluble. The polymer-bound DNA is then separated from theliquid mixture which comprises non-desirable soluble substances. DNA isthen released from the polymer by means of alkali addition. Thus themethod of the present invention requires only three steps: (a) contactof sample with buffer, (b) contact and incubation of mixture formed instep (a) with a weakly basic polymer, and (c) release of the DNA boundto polymer in step (b) by contact with alkali. The method eliminates theneed for extraction with alcohol or other solvent and toxic materialssuch as phenol or chloroform, and lysing agents are not used. The methodnot only simplifies DNA recovery, but also results in an improvement inyield of amplifiable target DNA. Although the method is preferably usedwith serum and blood as the sample, it is applicable to other bodyfluids including but not limited to urine, bile, spinal fluid, bronchiallavage (BAL), colonic washes, and stool. In addition, samples of anytype can be used, including those collected from animals, humans,environmental and microbial specimens.

In another aspect the present invention relates to amplification anddetection of target DNA using the method of DNA recovery describedhereinabove.

The inventive methods of the invention comprise the steps of:

A) at a pH of less than 7, contacting a sample suspected of containing anucleic acid with a water-soluble, weakly basic polymer in an amountsufficient to form a water-insoluble precipitate of the weakly basicpolymer with all nucleic acids present in the sample,B) separating the water-insoluble precipitate from the sample, andC) contacting the precipitate with a base to raise the solution pH togreater than 7, and thereby releasing the nucleic acids from the weaklybasic polymer,the weakly basic polymer comprising recurring units derived by additionpolymerization of one or more ethylenically unsaturated polymerizablemonomers having an amine group which can be protonated at acidic pH.

This invention also provides a method for the amplification anddetection of a target nucleic acid comprising:

I) providing a target nucleic acid using the steps of:

-   -   A) at a pH of less than 7, contacting a sample suspected of        containing a target nucleic acid with a water-soluble, weakly        basic polymer in an amount sufficient to form a water-insoluble        precipitate of the weakly basic polymer with all nucleic acids        present in the sample, including the target nucleic acid,    -   B) separating the water-insoluble precipitate from the sample,        and    -   C) contacting the precipitate with a base to raise the solution        pH to greater than 7, and thereby releasing the nucleic acids,        including the target nucleic acid, from the weakly basic        polymer,    -   the weakly basic polymer comprising recurring units derived by        addition polymerization of one or more ethylenically unsaturated        polymerizable monomers having an amine group which can be        protonated at acidic pH,        II) amplifying the target nucleic acid present among the        released nucleic acids, and        III) detecting the amplified target nucleic acid.        A test kit for amplification of a target nucleic acid comprises,        separately packaged:        a) an amplification reaction mixture comprising one or more        amplification reagents, and        b) a weakly basic polymer comprising recurring units derived by        addition polymerization of one or more ethylenically unsaturated        polymerizable monomers having an amine group which can be        protonated at acidic pH.

The present invention provides a rapid, simple and effective method forselectively isolating and providing nucleic acids for further treatment,such as hybridization assays or amplification procedures. This inventionovercomes the problems noted above relating to conventional isolationmeans, including the use of polyethyleneimine. In addition, the problemspresented by the use of polyethyleneimine combined with a fluorinatedphosphate surfactant are also avoided because the surfactant is notneeded. The sample preparation method of this invention is not tediousand requires a minimum of steps, thereby making it more readilyautomated. It usually can be carried out within about 15 minutes(preferably within 10 minutes).

These advantages are provided by using in place of the polyethyleneiminea “weakly basic” polymer which is cationic and water-soluble at acidicpH, but deprotonates at a basic pH which is significantly above the pKaof the polymer. By “weakly basic” is meant that the polymer pKa is lessthan 7, and more likely less than 6.5. Thus, the polymer can be used atlow pH to precipitate nucleic acids because of the ionic interaction ofthe cationic polymer and the anionic phosphate backbone of nucleicacids.

After removing noncomplexed materials, and upon a pH adjustment to basicconditions, the nucleic acids are released (or decomplexed) from theweakly basic polymer of the precipitate and available for furthertreatment, such as amplification. The amplification procedures can becarried out under basic conditions.

BRIEF DESCRIPTION OF THE DRAWING

FIG. 1 illustrates a standard curve for DNA as evaluated by TaqManamplification with the β-actin gene after 40 PCR cycles.

FIG. 2 ILLUSTRATES THE RESULTS OF ANALYSIS FOR A k-12 ras mutation asdetermined by gel electrophoresis after REMS-PCR in accordance withExample 7.

DETAILED DESCRIPTION OF THE INVENTION

The present invention is especially suited for the extraction anddetection of one or more target nucleic acids present in a sample of anytype collected from animals, humans, environmental or microbialspecimens. The nucleic acids so obtained can be further treated bysubjecting them to conventional hybridization assays, the procedures ofwhich are well known in the art (for example, U.S. Pat. No. 4,994,373,incorporated herein by reference with respect to the hybridizationtechnology).

However, for the sake of brevity, the remaining discussion will bedirected to preferred embodiments whereby the nucleic acids aresubjected to amplification procedures, particularly PCR. However, thescope of this invention is not intended to be so limited because otheramplification techniques (such as LCR) can be used also.

The general principles and conditions for amplification and detection ofnucleic acids using polymerase chain reaction are quite well known, thedetails of which are provided in numerous references including U.S. Pat.No. 4,683,195 (Mullis et al), U.S. Pat. No. 4,683,202 (Mullis), U.S.Pat. No. 4,965,188 (Mullis et al) and WO-A-91/12342. The noted U.S.patents are incorporated herein by reference. In view of the teaching inthe art and the specific teaching provided herein, a worker skilled inthe art should have no difficulty in practicing the present invention bycombining the preparatory method of this invention with polymerase chainreaction procedures, or with any other amplification procedure known inthe art.

Other amplification procedures which can be used in the practice of thisinvention include, but are not limited to, ligase chain reaction asdescribed, for example, in EP-A-0 320 308 (published December, 1987) andEP-A-0 439 182 (published January, 1990).

Test specimens (“samples”) can include body fluids or other materialscontaining genetic DNA or RNA. The target nucleic acid can be extractedfrom any suitable human, animal, microbial, viral or plant source.

The advancement disclosed herein contemplates that prior to contact withthe weakly basic polymer defined herein, no extraction of nucleic acidsfrom the specimen is required. While the prior art teaches variouslysing procedures known in the art (including those described by Laureet al in The Lancet, pp. 538-540 (Sep. 3, 1988), Maniatis et al,Molecular Cloning: A Laboratory Manual, pp. 280-281 (1982),Gross-Belland et al in Eur. J. Biochem., 36, 32 (1973) and U.S. Pat. No.4,965,188 (noted above)). Extraction of DNA from whole blood orcomponents thereof is described, for example, in EP-A-0 393 744(published Oct. 24, 1990), U.S. Pat. No. 5,231,015 (Cummins et al) andU.S. Pat. No. 5,334,499 (Burdick et al); the lysing procedure beingdependent upon the type of specimen being used as the source of nucleicacids; a preferred lysing procedure includes heating the specimen in thepresence of a suitable nonionic surfactant, a number of which are wellknown in the art. Another useful lysing procedure is described in U.S.Ser. No. 08/063,169 (filed May 18, 1993 by Ekeze and Kerschner) wherebya whole blood specimen is mixed with a buffered solution of ammoniumchloride, followed by additional steps which includes a second mixingwith ammonium chloride, the methods of the instant invention do notemploy a lysing step.

The sample, first diluted and admixed with a buffer at below pH of about7.0, is admixed with a weakly basic polymer (defined below) in an amountsufficient to complex with all nucleic acids present in the sample,forming a water-insoluble precipitate. This polymer is water-soluble atacidic pH. Generally, the amount of polymer present is at least about0.01 weight percent, with from about 0.05 to about 0.5 weight percentpreferred. Of course, a skilled artisan would know how to adjust theamount of polymer to accommodate any quantity of nucleic acids. Mixingcan be carried out in any suitable manner for up to 30 minutes(generally less than 5 minutes) and at any suitable temperature(generally from 15° to 35° C.

Suitable buffers for admixture with sample include those buffers havinga pKa less than 7, more preferably less than pKa 6.5, including MES(2-[N-Morpholino]ethanesulfonic acid) at pK 6.1, BIS-TRIS(bis[2-Hydroxyethyl]iminotris[hydroxymethyl]methane;2-bis[2-hydroxyethyl]amino-2-[hydroxymethyl]-1,3-propanediol) at pK 6.5,ADA (N-[2-Acetamido]-2-iminodiacetic acid;N-[Carbamoylmethyl]iminodiacetic acid) at pK 6.6, ACES(N-[Carbamoylmethyl]-2-aminoethanesulfonic acid;N-[2-Acetamido]-2-aminoethanesulfonic acid) at pK 6.8, PIPES(piperazine-N,n′-bis[2-ethanesulfcid]; 1,4-piperazinediethanesulfonicacid) at pK 6.8, MOPSO (3-[N-Morpholino]-2-hydroxypropanesulfonic acid)at pK 6.9, BIS-TRIS Propane(1,3-bis[tris(Hydroxymethyl)methylamino]propane) at pK 6.8, PBS(phosphate buffered saline), and TRIS (tris(hydroxymethyl)aminomethane),the weakly basic polymer can be used in its water-soluble free form, orattached to a water-insoluble substrate, such as in an affinity column,or attached to polymeric, glass or other inorganic particles. Thus, thepolymers can be attached using conventional means (for example,absorption, covalent bonds or specific binding reactions) to a suitablesubstrate, including glass, polymeric or magnetic particles, filters orfilms. Where the weakly basic polymer is water-insoluble even at basicpH, it can be removed through filtration, centrifugation or otherconventional means after the nucleic acids are released.

While bound to the weakly basic polymer, however, the nucleic acids arenot useful. It is then necessary to separate the water-insolubleprecipitate from the remainder of the sample which may containconsiderable cellular debris and excess polymer. This separation can beachieved using any of various conventional procedures, includingcentrifugation or filtration after which the liquid is discarded.Centrifugation is preferred in the practice of this invention and can becarried out at greater than about 1,000×g, for one minute to 5 minutes.

After the separation step, the nucleic acids can be decomplexed orreleased from the weakly basic polymer, by contacting the precipitatewith a base, with or without heating. Strong bases may be used withoutheating, and they include, but are not limited to, sodium hydroxide,potassium hydroxide, ammonium hydroxide, lithium hydroxide, sodiumcarbonate, sodium bicarbonate, a tertiary amine (such as triethylamine,diisopropylethylamine and lutidine), tricine, bicine or any otherorganic or inorganic base which would be readily apparent to one skilledin the art. Useful weaker bases may include basic buffers such astris(hydroxymethyl)aminomethane (or acid addition salts thereof),N,N-bis(2-hydroxyethyl)glycine, N-tris(hydroxymethyl)methyl-glycine, andothers well known in the art. Heating may be necessary when weaker basesare used.

Such heating can be carried out for up to 15 minutes (generally lessthan 5 minutes) at a temperature that is at least about 50° C., andpreferably is from about 95° to about 125° C., under suitable pressure.As used in this paragraph, “about” refers to +/−0.5° C.

In preferred embodiments, weaker bases can be used with heating, torelease the nucleic acids from the precipitate. This provides a solutioncontaining nucleic acids which are ready for amplification withoutfurther treatment. Such weaker bases may be buffers, such astris(hydroxymethyl)aminomethane hydrochloride.

In some embodiments, the polymers used in such embodiments are those(defined below) which are water-insoluble even at basic pH. Suchpolymers can be removed from the system after release of nucleic acidsand prior to amplification if desired.

The resulting solution containing released nucleic acids has a basic pH.In some instances, the nucleic acids can be further treated without anyfurther adjustment in pH. In other embodiments where a strong base isused, the pH of the solution may be adjusted (generally downward) tofrom about 6 to about 9 (preferably from about 7.5 to about 9), usingany suitable acid or buffer, such as tris(hydroxymethyl)aminomethanehydrochloride, N,N-bis(2-hydroxyethyl)glycine,N-tris(hydroxymethyl)methylglycine and others which would be readilyapparent to one skilled in the art. The amounts of such materials neededto achieve the desired pH would be readily apparent to one skilled inthe art.

At basic pH, the polymer used for capture of nucleic acids can be eitherwater-soluble or water-insoluble, and monomers needed for providing suchproperties are described below.

The described method of capturing and releasing nucleic acids of thisinvention is typically carried out within about 20 minutes, andpreferably within about 10 minutes.

As used herein, unless otherwise noted, the modifier “about” refers to avariance of 110% of the noted values. When used with pH values, “about”refers to +/−0.5 pH unit.

In a preferred embodiment of this invention, a method for theamplification and detection of a target nucleic acid comprises:

I) providing a sample suspected of containing a target nucleic acid,II) subjecting the target nucleic acid to the steps of:

-   -   A) at a pH of less than 7, contacting the target nucleic acid        with a water-soluble, weakly basic polymer in an amount        sufficient to form a water-insoluble precipitate of the weakly        basic polymer with all nucleic acids present in the sample,        including the target nucleic acid,    -   B) separating the water-insoluble precipitate from the sample,        and    -   C) contacting the precipitate with a base to raise the solution        pH to greater than 7, and thereby releasing the nucleic acids,        including the target nucleic acid, from the weakly basic        polymer,    -   the weakly basic polymer comprising recurring units derived by        addition polymerization of one or more ethylenically unsaturated        polymerizable monomers having an amine group which can be        protonated at acidic pH,        III) without further adjustment of pH, amplifying the released        target nucleic acid, and        IV) detecting the amplified target nucleic acid.

In the foregoing method, it is still more preferred that the weaklybasic polymer is water-insoluble at basic pH, and the method furthercomprises the step of removing the water-insoluble polymer after releaseof the target nucleic acid but prior to amplification thereof.

The weakly basic polymer used in the practice of this invention isprepared from one or more ethylenically unsaturated polymerizablemonomers, at least one of which has an amine group which can beprotonated at acidic pH. Thus, at acidic pH, the polymer is protonatedto form the acid addition salt of the amine. At basic pH, the polymerexists as the free base.

Particular “weakly basic groups” which can be a part of polymerizablemonomers useful in this invention include, but are not limited to,cyclic amine groups, or primary, secondary or tertiary aminoalkyl groupswhich can be protonated at acidic pH. Useful cyclic amine groupsinclude, but are not limited to, imidazolyl, isoxazolyl, pyridyl,piperidyl, piperazinyl, pyrazolyl, triazolyl, tetrazolyl, oxadiazolyl,pyridazinyl, pyrimidyl, pyrazinyl, quinolinyl and quinazolinyl groups.The preferred groups are cyclic groups which are aromatic, and theimidazolyl group is most preferred. Useful aminoalkyl or cyclic aminegroups are linked to vinyl groups of the monomers using convenientlinking groups including alkylene, amido or ester groups, and multiplealkylene groups can be linked together with imino, oxy, amide, carbonylor ester groups.

Generally useful polymers for capturing nucleic acids are comprised ofrecurring units derived by addition polymerization of:

a) from about 15 to 100 weight percent of a water-soluble, weakly basicethylenically unsaturated polymerizable monomer having at least onegroup which can be protonated at acidic pH and which is selected fromthe group consisting of aminoalkyl, imidazolyl, isoxazolyl, pyridyl,piperidyl, piperazinyl, pyrazolyl, triazolyl, tetrazolyl, oxadiazolyl,pyridazinyl, pyrimidyl, pyrazinyl, quinolinyl and quinazolinyl,b) from 0 to about 35 weight percent of a nonionic, hydrophilicethylenically unsaturated polymerizable monomer, andc) from 0 to about 85 weight percent of a nonionic, hydrophobicethylenically unsaturated polymerizable monomer.

Preferably, the weakly basic polymer is comprised of recurring units offrom about 20 to about 100 weight percent of a), from 0 to about 25weight percent of b), and from 0 to about 80 weight percent of c).

A more specific class of monomers useful in a) above are thoserepresented by the structure (I):

wherein R³ is hydrogen or methyl, and X is oxy or imino. In addition, R⁴is a divalent hydrocarbon linking group having from 1 to 8 carbon andhetero atoms in the chain and comprising one or more alkylene groups(such as methylene, ethylene, n-propylene, isopropylene andn-pentylene), providing that when there is more than one alkylene group,they are linked together in R⁴ with one or more carbonyl, oxy, imino,ester or amido groups in any operable combination. By “operablecombination” is meant that those groups can be combined with thealkylene groups in any chemically possible configuration, and can beused in combination (connected to each other) in chemically possibleways (such as oxycarbonyl, carbonamido and others readily apparent toone skilled in the art). It is also to be understood that R⁴ can beterminated (or connected to R⁵) with a carbonyl, oxy, imino, ester oramido group.

R⁵ is a cyclic amine or primary, secondary or tertiary aminoalkyl group,as defined above, which can be protonated at acidic pH.

Examples of useful type a) monomers include, but are not limited to,1-vinylimidazole, 2-methyl-1-vinylimidazole, 2-vinylpyridine,1-hydroxy-6-vinyl-1H-benzotriazole, 2-aminoethyl methacrylatehydrochloride, 2-aminoethyl acrylate hydrochloride,N-(3-aminopropyl)methacrylamide, 2-vinylquinoline,N-(3imidazolylpropyl)methacrylamide,N-(2-imidazolylethyl)methacrylamide, N-(3-imidazolylpropyl)acrylamide,N-(1,1-dimethyl-3-N-imidazolylpropyl)acrylamide,N-(imidazolylmethyl)acrylamide, 1-vinylpyrrolidinone,3-(N,N-dimethylamino)propyl metharcylate and acid addition salts of thenoted free bases.

A class of novel monomers of type a) of this invention can be used toprepare either homopolymers or copolymers. These monomers are defined bythe structure (II):

wherein R is hydrogen or methyl. Preferably, R is methyl. In addition,R¹ is branched or linear alkylene of 1 to 3 carbon atoms (such asmethylene, ethylene, trimethylene or propylene). Preferably, R¹ isalkylene of 2 or 3 carbon atoms. More preferably, R¹ is trimethylene.

Particularly useful monomers having structure (II) include, but are notlimited to, N-(3-imidazolylpropyl)methacrylamide,N-(2-imidazolylethyl)methacrylamide, N-(3-imidazolylpropyl)acrylamide,N-(1,1-dimethyl-3-N-imidazolylpropyl)acrylamide,N-(imidazolylmethyl)acrylamide, and their acid addition salts. Of thenovel monomers described herein, the first compound is most preferred.

Preferred type a) monomers include 1-vinylimidazole andN-2-methyl-1-vinylimidazole.

If the monomers of type a) have low or no water solubility, they canalso be polymerized in the form of their acid addition salts (such asthe hydrochloride or hydrobromide).

Monomers identified as type b) monomers are those which are definedherein as “hydrophilic”, meaning those which, when homopolymerized,provide homopolymers which are water-soluble at pH 7 or above.Generally, such monomers have hydrophilic groups such as hydroxy, amine(primary, secondary, tertiary and cyclic), amide, sulfonamide andpolyethyleneoxy groups, but it is not necessary that they comprise suchgroups if the noted homopolymer water-solubility parameter is met.

Representative monomers of type b) include, but are not limited to,acrylamide, 2-hydroxyethyl acrylate, 2,3-dihydroxypropyl acrylate,2,3-dihydroxypropyl methacrylate, poly(ethyleneoxy)ethyl methacrylate(having 2 to 10 ethyleneoxy groups), and N,N-dimethylacrylamide. Apreferred monomer is acrylamide.

Monomers identified as type c) monomers are those which are definedherein as “hydrophobic”, meaning those which, when homopolymerized,provide homopolymers which are water-insoluble at pH 7 or above,irrespective of the type of pendant groups they may possess.

Representative monomers of type c) include, but are not limited to,methacrylamide, 2-hydroxyethyl methacrylate, N-t-butylmethacrylamide,ethyl acrylate, methyl acrylate, butyl acrylate, methyl methacrylate,styrene, vinyltoluene and other vinyl aromatics and others which wouldbe readily apparent to one skilled in the art. A preferred monomer is2-hydroxyethyl methacrylate.

The monomers of types a), b) and c) which are not novel are generallyreadily available from commercial sources, or prepared usingconventional procedures and starting materials.

The novel monomers of structure (II) can be prepared generally bycondensation of a 1-(aminoalkyl)imidazole with a (meth)acryloyl chlorideusing appropriate conditions which would be readily apparent to oneskilled in the art. A representative preparation of a preferred monomeris provided below preceeding the examples. More details about suchmonomers can be obtained from commonly assigned U.S. Pat. No. 5,434,270,Ponticello et al., entitled “Weakly Basic Polymerizable Monomers andPolymers Prepared Therefrom”.

The homopolymers and copolymers described herein can be prepared usingconventional solution polymerization techniques which are well known inthe art, although there are certain preferred conditions which areillustrated in the preparatory methods provided below preceding theExamples. The ratio of various monomers can be adjusted, as one skilledin the art would know, to provide polymers which are eitherwater-soluble or water-insoluble at basic pH, as long as such polymersremain water-soluble at acidic pH.

Solution polymerization generally involves dissolving the monomers in asuitable solvent (including water or various water-miscible organicsolvents) and polymerizing in the presence of a suitable free radicalinitiator. The resulting polymer is water-soluble at acidic pH, so it isprecipitated using a solvent such as acetone, purified and redissolvedin water for future use.

Particularly useful polymers described herein include, but are notlimited to, poly[N-(3-imidazolylpropyl)methacrylamidehydrochloride-co-acrylamide], poly[N-(3-imidazolylpropyl)methacrylamidehydrochloride-co-2-hydroxyethyl methacrylate], poly(1-vinylimidazole),poly(2-aminoethyl methacrylate hydrochloride-co-2-hydroxyethylmethacrylate), poly(1-vinylimidazole hydrochloride-co-2-hydroxyethylmethacrylate),poly[N-(1,1-dimethyl-3-imidazolylpropyl)acrylamide]poly(N-2-methyl-1-vinylimidazole) and acid addition salts of the free base polymers.

In preferred embodiments, the polymers used are water-insoluble at basicpH. Such polymers are prepared using type a) monomers as well as type c)monomers but with limited amounts (less than 15 weight of type b)monomers to prevent solubilization of the polymer at basic pH.Representative polymers of this type include, but are not limited to,poly[N-(3-imidazolylpropyl)-methacrylamidehydrochloride-co-2-hydroxyethyl methacrylate], poly(1-vinylimidazole),poly(2-aminoethyl methacrylate hydrochloride-co-2-hydroxyethylmethacrylate) and poly(1-vinylimidazole hydrochloride-co-2-hydroxyethylmethacrylate).

The present invention is also directed to the amplification or detectionof one or more specific nucleic acid sequences present in one or moretarget nucleic acids released as noted above. Moreover, a plurality oftarget nucleic acids can be amplified and detected simultaneously byusing a corresponding set of primers and detection means for eachspecific nucleic acid. Multiple sequences in the same nucleic acid canalso be amplified and detected.

A “PCR reagent” refers to any of the reagents generally considereduseful in PCR, namely a set of primers for each target nucleic acid, aDNA polymerase, a DNA polymerase cofactor and two or moredeoxyribonucleoside-5′-triphosphates (dNTP's).

As used herein in referring to primers or probes, the term“oligonucleotide” refers to a molecule comprised of four or moredeoxyribonucleotides or ribonucleotides, and preferably more than ten.Its exact size is not critical but depends upon many factors includingthe ultimate use or function of the oligonucleotide. The oligonucleotidemay be derived by any method known in the art.

The term “primer” refers to an oligonucleotide, whether naturallyoccurring or synthetically produced, which is capable of acting as apoint of initiation of synthesis when placed under conditions in whichsynthesis of a primer extension product complementary to a nucleic acidstrand (that is, template) is induced. Such conditions include thepresence of nucleotides (such as the four standarddeoxyribonucleoside-5′-triphosphates), a DNA polymerase and a DNApolymerase cofactor, and suitable temperature and pH. Normally, suchconditions are what are known in the art as “high stringency” conditionsso that nonspecific amplification is minimized. The primer must be longenough to initiate the synthesis of extension products in the presenceof the DNA polymerase. The exact size of each primer will vary dependingupon the use contemplated, the complexity of the targeted sequence,reaction temperature and the source of the primer. Generally, theprimers used in this invention will have from 10 to 60 nucleotides.

Primers useful herein can be obtained from a number of sources orprepared using known techniques and equipment, including for example, anABI DNA Synthesizer (available from Applied Biosystems) or a Biosearch8600 Series or 8800 Series Synthesizer (available fromMilligen-Biosearch, Inc.) and known methods for their use (for exampleas described in U.S. Pat. No. 4,965,188). Naturally occurring primersisolated from biological sources are also useful (such as restrictionendonuclease digests). As used herein, the term “primer” also refers toa mixture of primers. Thus, each set of primers for a given targetnucleic acid may include two or more primers for each opposing targetstrand.

One or both primers can be labeled with the same or different label fordetection or capture of amplified product. Procedures for attachinglabels and preparing primers are well known in the art, for example, asdescribed by Agrawal et al, Nucleic Acid Res., 14, pp. 6227-45 (1986),U.S. Pat. No. 4,914,210 (Levenson et al) relating to biotin labels, U.S.Pat. No. 4,962,029 (Levenson et al) relating to enzyme labels, and thereferences noted therein. Useful labels also include radioisotopes,electron-dense reagents, chromogens, fluorogens, phosphorescentmoieties, ferritin and other magnetic particles (see U.S. Pat. No.4,795,698 of Owen et al and U.S. Pat. No. 4,920,061 of Poynton et al),chemiluminescent moieties (such as luminol), and other specific bindingspecies (avidin, streptavidin, biotin, sugars or leetins). Preferredlabels are enzymes, radioisotopes and specific binding species (such asbiotin). Useful enzymes include, glucose oxidase, peroxidases, uricase,alkaline phosphatase and others known in the art and can be attached tooligonucleotides using known procedures. Reagents to provide acolorimetric or chemiluminescent signal with such enzymes are wellknown.

Where the label is an enzyme such as a peroxidase, at some point in theassay, hydrogen peroxide and suitable dye-forming compositions are addedto provide a detectable dye. For example, useful dye-providing reagentsinclude tetramethylbenzidine and derivatives thereof, and leuco dyes,such as water-insoluble triarylimidazole leuco dyes (as described inU.S. Pat. No. 4,089,747 of Bruschi), or other compounds which react toprovide a dye in the presence of peroxidase and hydrogen peroxide.Particularly useful dye-providing compositions are described in EP-A-0308 236 (published Mar. 22, 1989). Chemiluminescent signals in responseto a peroxidase label can also be generated using the appropriatereagents.

If one or both primers are biotinylated, the amplified nucleic acid canbe detected using detectably labeled avidin or an equivalent thereof(such as streptavidin). For example, avidin can be conjugated with anenzyme, or have a radioisotope using known technology. Biotin on theamplified product complexes with the avidin, and appropriate detectiontechniques to detect a radioactive, calorimetric or chemiluminescentsignal are used.

As used herein, a capture “probe” is an oligonucleotide which issubstantially complementary to a nucleic acid sequence of one or morestrands of the target nucleic acid, and which is used to insolubilizethe amplified nucleic acid. The probe oligonucleotide is generallyattached to a suitable water-insoluble substrate such as polymeric orglass beads, microtiter plate well, thin polymeric or cellulosic film orother materials readily apparent to one skilled in the art. Theoligonucleotide is generally from about 12 to about 40 nucleotides inlength, although the length is not critical.

A DNA polymerase is an enzyme which will add deoxynucleosidemonophosphate molecules to the 3+−hydroxy end of the primer in a complexof primer and template, but this addition is in a template dependentmanner (that is, dependent upon the specific nucleotides in thetemplate). Many useful DNA polymerases are known in the art. Preferably,the polymerase is “thermostable”, meaning that it is stable to heat,especially the high temperatures used for denaturation of DNA strands.More particularly, the thermostable DNA polymerases are notsubstantially inactivated by the high temperatures used in PCR asdescribed herein.

A number of thermostable DNA polymerases have been reported in the art,including those mentioned in detail in U.S. Pat. No. 4,965,188 (notedabove) and U.S. Pat. No. 4,889,818 (Gelfand et al), incorporated hereinby reference.

Particularly useful polymerases are those obtained from various Thermusbacterial species, such as Thermus aquaticus, Thermus thermophilus,Thermus filiformis or Thermus flavus. Other useful thermostablepolymerases are obtained from a variety of other microbial sourcesincluding Thermococcus literalis, Pyrococcus furiosus, Thermotoga sp.and those described in WO-A-89/06691 (published Jul. 27, 1989). Someuseful polymerases are commercially available. A number of techniquesare known for isolating naturally-occurring polymerases from organisms,and for producing genetically engineered enzymes using recombinanttechniques, as noted in the art cited in this paragraph.

A DNA polymerase cofactor refers to a nonprotein compound on which theenzyme depends for activity. A number of such materials are knowncofactors including manganese and magnesium salts. Useful cofactorsinclude, but are not limited to, manganese and magnesium chlorides,sulfates, acetates and fatty acid salts (for example, butyric, caproic,caprylic, capric and lauric acid salts). The smaller salts, that ischlorides, sulfates and acetates, are preferred.

Also needed for PCR are two or moredeoxyribonucleotide-5′-triphosphates, such as dATP, dCTP, dGTP, dUTP ordTTP. Usually, dATP, dCTP, dGTP and dTTP are all used in PCR. Analoguessuch as dITP and 7-deaza-dGTP are also useful.

Also useful in the practice of the invention is an antibody specific tothe DNA polymerase, which antibody inhibits its enzymatic activity attemperatures below about 50° C., but which antibody is deactivated athigher temperatures. Representative monoclonal antibodies having theseproperties are described in U.S. Pat. No. 5,338,671 (Scalice et al),incorporated herein by reference. Antibody fragments can be used inplace of the whole molecule if they have equivalent properties.

The PCR reagents described herein are provided and used in PCR insuitable concentrations to provide amplification of the target nucleicacid. The minimal amounts of DNA polymerase is generally at least about1 unit/100 μl of solution, with from about 4 to about 25 units/100 μlbeing preferred. A “unit” is defined herein as the amount of enzymeactivity required to incorporate 10 nmoles of total nucleotides (dNTP's)into an extending nucleic acid chain in 30 minutes at 74° C. Theconcentration of each primer is at least about 0.075μ molar with fromabout 0.2 to about 1μ molar being preferred. All primers are present inabout the same amount (within a variation of 10% of each). The cofactoris generally present in an amount of from about 1 to about 15 mmolar,and each dNTP is generally present at from about 0.1 to about 3.5 mmolarin the reaction mixture. As used in this paragraph, the modifier “about”refers to a variance of +/−10% of the noted value.

The PCR reagents can be supplied individually, or in a buffered solutionhaving a pH in the range of from about 7 to about 9 using any suitablebuffer.

Since the target nucleic acid to be amplified and detected is usually indouble strand form, the two strands must be separated (that is,denatured) before priming can take place. This can occur during theextraction process, but preferably, it occurs in a separate stepafterwards. Heating to a suitable temperature (identified as “firsttemperature” or T₁ herein) is a preferred means for denaturation.Generally, this first temperature is in the range of from about 85° toabout 100° C. for a suitable time, for example from 1 to about 240seconds (preferably 1 to about 40 seconds). This initial denaturationstep can also be included in the first amplification cycle. In suchinstances, denaturation may be longer in the first cycle (for example,up to 240 seconds) whereas later cycles can have much shorterdenaturation steps (for example, up to 30 seconds).

The denatured strands are then primed with the appropriate sets ofprimers by cooling the reaction mixture to a second temperature, T₂,which is generally within the range of from about 55° to about 70° C. Itis desired that cooling is done as quickly as possible, but withpresently known equipment, it generally takes place over a time periodof from about 5 to about 40 seconds, and more preferably for from about5 to about 20 seconds.

Once the denatured strands are cooled, the reaction mixture containingthe PCR reagents is incubated at a third temperature, T₃, generally forfrom 1 to about 120 seconds, and preferably for from 1 to about 80seconds, to effect formation of primer extension products. Generally,the third temperature is within the range of from about 55° to about 74°C. Preferably, it is within the range of from about 62° to about 70° C.

In a most preferred embodiment, the second and third temperatures arethe same and are within the range of from about 62° to about 70° C.Thus, priming and primer extension are preferably carried out in thesame step.

Thus, an amplification cycle comprises the denaturation, priming (orannealing) and primer extension steps described above. Generally, atleast 15 of such amplification cycles are carried out in the practice ofthis invention with the maximum number of cycles being within thediscretion of the particular user. In most instances, 15 to 50amplification cycles are used in the method with 15 to 40 cycles beingpreferred. Each amplification cycle is generally from about 20 to about360 seconds, with a cycle time of from about 30 to about 120 secondsbeing preferred and from about 30 to about 90 seconds being morepreferred. However, longer or shorter cycle times can be used ifdesired.

When used in reference to time for a given step in the amplificationprocedure, the term “about” refers to +/−10% of that time limit.Moreover, when used in reference to temperatures, the term “about”refers to +/−0.5° C.

Detection of amplified products can be accomplished using any knownprocedure, including Southern blotting techniques, as described in U.S.Pat. No. 4,965,188 (noted above), or by use of labeled probes orprimers, as is known in the art.

Alternatively to the embodiments described above, the amplified productscan be detected using a labeled oligonucleotide which is complementaryto one of the primer extension products.

All reagents for performing the TaqMan assay were purchased from AppliedBiosystems, a Division of Perkin-Elmer Co., Foster City, Calif.,including: β-Actin detection reagents (cat. no. 401846), DNA templatereagents (cat. no. 401970) and TaqMan PCR Core Reagent Kit (cat. no.N808-0228). Assays were performed using the PCR Master mix and thermalcycling profiles for the β-Actin TaqMan assay provided by themanufacturer. One microliter of DNA template reagent was added to 49 μLof PCR β-Actin Master mix in an ABI Prism 7700 Sequence Detection System(Applied Biosystems) and fluorescence was measured during the 40 PCRcycles.

FIG. 1 shows a calibration curve for different starting levels of DNAversus Threshold cycle count, which is a value determined by theinstrument and represents the estimated number of PCR cycles at which apreselected fluorescence signal will be obtained. Thus, the TaqMan assayfor a β-Actin gene fragment provides a good analytical tool formeasuring DNA concentration present in a sample.

In the examples that follow, DNA from the single copy (per cell) β-Actingene was extracted from the indicated samples according to the method ofthe invention or using the indicated prior art method which utilizes acell lysing reagent. β-Actin DNA extracted thereby was amplified usingthe PCR Master Mix and thermal cycling profiles and TaqMan detection asper the manufacturer's recommended procedures.

In the heterogeneous detection systems of this invention, the amplifiedproducts are captured on a water-insoluble substrate of some kind, andthe other materials in the reaction mixture are removed in a suitablemanner, such as by filtration, centrifugation, washing or anotherseparation technique.

Capture probes can be attached to water-insoluble supports using knownattachment techniques (including absorption and covalent reactions). Onesuch technique is described in EP-A-0 439 222 (published Sep. 18, 1991).Other techniques are described, for example, in U.S. Pat. No. 4,713,326(Dattagupta et al), U.S. Pat. No. 4,914,210 (Levenson et al) and EP-B-0070 687 (published Jan. 26, 1983). Useful separation means includefiltration through membranes such as polyamide microporous membranescommercially available from Pall Corporation.

However, any useful solid support can be used to anchor the captureprobe and eventual hybridization product, including microtiter plates,test tubes, beakers, magnetic or polymeric particles, metals, ceramics,and glass wool to name a few. Particularly useful materials are magneticor polymeric particles having reactive groups useful for covalentlyattaching the capture probe. Such particles are generally from about0.001 to about 10μ meters. Further details about examples of suchmaterials are provided in U.S. Pat. No. 4,997,772 (Sutton et al), U.S.Pat. No. 5,147,777 (Sutton et al), U.S. Pat. No. 5,155,166 (Danielson etal) and U.S. Pat. No. 4,795,698 (Owen et al), all incorporated herein byreference.

The capture probe can be affixed to a flat support such as a polymericfilm, membranes, filter papers, or resin-coated or uncoated paper.Capture probe affixed to polymeric particles can also be immobilized onsuch flat supports in a suitable manner, for example, as dried deposits,or adhered by heat fusion or with adhesives. The capture probe can beaffixed, for example, to a flat support in the self-contained testdevice of this invention. Other details of such materials are providedin EP-A-0 408 738 (published Jan. 23, 1991), WO 92/16659 (published Oct.1, 1992) and U.S. Pat. No. 5,173,260 (Sutton et al).

The capture probes can be arranged on a suitable support in anyconfiguration, for example rows of round deposits or stripes.

The present invention can also be used in what are known as“homogeneous” amplification procedures in which target nucleic acids aredetected without the need for capture reagents. The details of suchassays are known in the art, such as in EP-A-0 487 218 (published May27, 1992) and EP-A-0 512 334 (published Nov. 11, 1992).

The amplification reaction composition can be included as oneindividually packaged component of a test kit useful for variousamplification assays. The kit can include other reagents, solutions,equipment and instructions useful in the method of this invention,including capture reagents immobilized on a water-insoluble substrate,wash solutions, detection reagents and other materials readily apparentto one skilled in the art. In addition, the test kit can include aseparately packaged weakly basic polymer as described above, buffers,weak or strong bases and other reagents needed for either or bothamplification and specimen sample preparation. The test kit can alsoinclude a test device containing one or more other kit components. Thistest device is preferably “self-contained” as that term is understood inthe art. Other kits can include the weakly basic polymer describedherein and one or more reagents (such as detection or capture probes)used in hybridization assays.

The following examples are included to illustrate the practice of thisinvention, and are not meant to be limiting in any way. All percentagesare by weight unless otherwise noted.

Materials and Methods for Examples Preparation ofN-(3-Imidazolylpropyl)-methacrylamide

This procedure shows the preparation of a novel monomer of structure(I), identified above, but the preparation is representative of howother monomers within the scope of this invention could readily beprepared.

A solvent mixture was prepared by mixing water (100 ml) containingsodium hydroxide (12.8 g, 0.32 mole) and dichloromethane (200 ml)containing 1-(3-aminopropyl)imidazole (37.5 g, 0.3 mole), and cooled inan ice bath. To this cooled mixture was added all at once, methacryloylchloride (34.8 g, 0.3 mole) in dichloromethane (100 ml) with vigorousstirring under a nitrogen atmosphere. Heat was evolved with thetemperature of the mixture rising to about 60° C., and the mixture wasvigorously stirred for another 10 minutes, and then the organic layerwas allowed to separate. The water layer was extracted twice withdichloromethane (100 ml each time). The combined organic solution (theorganic solvent layer and extracts) was washed with saturated sodiumchloride (100 ml), dried over anhydrous sodium sulfate, filtered, andthe solvent was removed. The residue was dissolved in chloroform (50ml), followed by the addition of ethyl ether (50 ml) to the cloud point.

The resulting reaction product crystallized at about 0° C., and wasfiltered to give a white solid having a melting point of 45°-46° C. Theyield was 70%.

Analytical data included: m/e (M-193),

¹H NMR (DMSO d6) 1.8 (m, 2H,C—CH₂—C,CH₃), 3.02 (m, 2H,N—CH₂), 3.95 (t,2H, im-CH₂), 5.25 and 5.6 (AB, 2H, vinyl-CH₂), 6.82 and 7.15 (AB, 2H,4,5-H of im), 7.6 (s, 1H, 2-H of im), 7.95 (m, 1H, NH).

Preparation of Homopolymer

A preferred homopolymer prepared from a novel monomer described hereinwas prepared by adding 2,2′-azobis(2-methylpropionitrile) (300 mg) to asolution of N-(3-imidazolylpropyl)methacrylamide (12.5 g, 0.065 mole) inwater (90 ml) and isopropanol (10 ml), maintained under a nitrogenatmosphere. The resulting solution was heated, while being stirred, to65°-70° C. in a water bath for 3 hours. After about 1.5 hours of thattime, concentrated HCl (3 ml) was added, and the stirring was continuedunder nitrogen for the remaining time. The solution was thenconcentrated on a rotary evaporator to about 25 ml, and the resultingpolymer product was precipitated in acetone (over 4 liters), filteredand dissolved in deionized water (80 ml). The solution contained 12%solids.

Preparation of First Copolymer

Poly[N-(3-imidazolylpropyl)methacrylamide hydrochloride-co-acrylamide](90:10 weight ratio) was prepared by adding2,2′-azobis(2-methylpropionitrile) (400 mg) to a solution ofN-(3-imidazolylpropyl)methacrylamide (18 g, 0.09 mole) and acrylamide (2g, 0.028 mole) in deionized water (120 ml) and isopropanol (15 ml),maintained under a nitrogen atmosphere. The solution was heated to65°-70° C. with stirring for 4 hours, followed by addition of dilute HClto lower the pH to about 2. Stirring and heating were continued foranother hour, and the solution was then allowed to reach roomtemperature overnight.

The solution was concentrated to about 75 ml using a rotary evaporator,and the resulting polymer was precipitated in acetone (about 4 liters),filtered and dissolved in deionized water (150 ml). Furtherconcentration to about 125 ml was carried out to remove residualacetone. The polymer was present at 15.5% solids.

Preparation of Second Copolymer

Poly[2-aminoethyl methacrylate hydrochloride-co-2-hydroxyethylmethacrylate] (20:80 weight ratio) was prepared by adding2,2′-azobis(2-methylpropionitrile) (400 mg) to a solution of2-aminoethyl methacrylate hydrochloride (4 g, 0.02 mole) and2-hydroxyethyl methacrylate (16 g, 0.12 mole) in deionized water (180ml) and ethanol (20 ml), maintained under a nitrogen atmosphere. Thesolution was heated to 65°-70° C. with stirring for 4 hours. Stirringand heating were continued for another hour, and the solution was thenallowed to reach room temperature overnight.

The resulting polymer was precipitated in acetone (about 4 liters),filtered and dissolved in deionized water (150 ml). Furtherconcentration to about 125 ml was carried out to remove residualacetone. The polymer was present at 5.6% solids.

Preparation of Third Copolymer

Poly[1-vinylimidazole-co-2-hydroxyethyl methacrylate] (50:50 weightratio) was prepared by adding 2,2′-azobis(2-methylpropionitrile) (350mg) to a solution of 1-vinylimidazole (10 g, 0.1 mole) and2-hydroxyethyl methacrylate (10 g, 0.077 mole) in N,N-dimethylformamide(160 ml), maintained under a nitrogen atmosphere. The solution washeated to 65°-70° C. with stirring for 7 hours.

After sitting at room temperature overnight, the polymer wasprecipitated in acetone (about 4 liters), filtered and dissolved indeionized water (200 ml) containing concentrated HCl (8.5 ml). Furtherconcentration was carried out to remove residual acetone. The polymerwas present at 12.4% solids.

Preparation of Fourth Copolymer

Poly(1-vinylimidazole-co-2-hydroxyethyl methacrylate) (25:75 weightratio) was prepared in a fashion like the “Third Copolymer”. Theresulting solution contained 13.7% solids.

Deoxyribonucleotides (dNTP's), tris(hydroxymethyl)aminomethane bufferand lyophilized calf thumus DNA were obtained from Sigma Chemical Co.

Gel electrophoresis was carried out by adding the amplification productmixture (6.75 μl) to agarose gels (2.5%) which had been prestained withethidium bromide (0.4 mg/ml final concentration). The gels wereelectrophoresed at about 8 volts/cm for about 1 hour using anelectrophoresis buffer (600 ml) containing ethidium bromide (0.4 mg/mlfinal concentration). The buffer was a mixture oftris(hydroxymethyl)aminomethane, borate and ethylenediaminetetraaceticacid. The resulting bands were compared to conventional molecular weightmarkers, and the product band intensity was scored (115-mer for HIV1 and383-mer for M. tuberculosis) on a 0 to 5 scale with 0 representing nodetectable signal and 5 representing the highest signal.

Other reagents and materials were obtained either from commercialsources or prepared using readily available starting materials andconventional procedures.

The invention has been described in detail with particular reference topreferred embodiments thereof, but it will be understood that variationsand modifications can be effected within the spirit and scope of theinvention.

Example 1 Capture and Release of DNA Using Weakly Basic Homopolymer

This example illustrates the practice of the present invention tocapture and release a nucleic acid using poly(1-vinylimidazole).

Various volumes of poly(1-vinylimidazole) [of a 1:10 dilution of 2.4%stock solution (pH 2.3)] were mixed with calf thymus DNA (100 μl, 0.5μg/μl) and vortexed to form a precipitate of nucleic acid and polymer.Centrifuging for 1 minute was then carried out. An additional amount ofpolymer (10 μl of the 2.4% stock solution) was added to each supernatantand the resulting mixtures were vortexed and centrifuged to determine ifthe first precipitation was quantitative. Table I below shows the amountof polymer used and the type of precipitation observed for each sample.

TABLE I Polymer First Second Volume Precipitation Precipitation (μl)Pellet Pellet 5 Barely Visible Large 10 Small to medium Small 25 LargeNot visible 50 Very large Not visible

It was observed that precipitation occurred under acidic conditions (pH2.3), and that 50 μl of the 1:10 dilution of polymer stock solutioncould be used to precipitate 100 μl of the calf thymus DNA solution (0.5μg/μl) Sigma Chemical Co., St. Louis, Mo., in a nearly quantitativefashion. This observation was also confirmed using conventional gelelectrophoretic methods.

Experiments were conducted to determine how to solubilize theprecipitate, thereby releasing the nucleic acid for later use. Table IIbelow shows the various pellet solubilization conditions attempted andthe resulting pellet size. The most useful technique was the use of heatin combination with basic pH (no pellet). Conventional gelelectrophoresis clearly indicated that at basic pH, the polymer andnucleic acids were present as free materials. Thus, the nucleic acidswere available for later use, such as in PCR.

TABLE II Solubilizing Conditions Pellet Size 50 μl NaCl (4 molar) None50 μl NaOH (50 mmolar) with heating at Small 55° C. for 5 minutes 50 μlNaOH (100 mmolar) with heating at None 55° C. for 5 minutes 50 μl NaOH(50 mmolar) with heating at None 100° C. for 10 minutes 50 μl NaOH (25mmolar) with heating at None 100° C. for 10 minutes 50 μl “TE” buffer*with heating at 100° C. Large for 10 minutes 50 μl water with heating at100° C. for 10 Large minutes *“TE” buffer includesethylenediaminetetraacetic acid (1 mmolar) intris(hydroxymethyl))aminomethane hydrochloride buffer (10 mmolar, pH 8)

Table III below shows the affect of pH on the formation of a precipitatebetween the polymer (50 μl of 1:10 dilution of stock solution) and calfthymus DNA (100 μl of 0.5 μg/μl solution). Acidic pH was clearlyrequired for effective capture of the nucleic acid by formation of aprecipitate (pellet).

TABLE III pH Pellet Size 2.3 Large 3 Large 4 Large 7 Clear, thick mass12 Barely visible

Example 2 Comparison of Polymer Capture of DNA with and Without a LysingReagent

The amount of DNA released from white blood cells contacted with alysing reagent (control) is compared with the amount released from cellsnot contacted with a lysing reagent (method of invention) but otherwisetreated identically.

In this example, 10 mL of blood was drawn into a VACUTAINER CPT cellPreparation Tube (Becton Dickinson Co., Franklin Lakes, N.J.), and thewhite blood cells (WBC) were separated by means of centrifugationaccording to the manufacturer's recommended protocol. Final WBCconcentration was determined to be 3.5×105/mL, based on microscopy.

Two hundred microliters of the WBC suspension was placed in each ofeight 1.5 mL microcentrifuge tubes (Eppendorf North America, Inc.,Madison, Wis.). The white blood cells were centrifuged, and washed 3times with phosphate buffered saline, (PBS, 0.15 M NaCl, and 0.05 Mpotassium phosphate buffer, pH 7.5).

Control—Use of Lysing Reagent

For samples contacted with lysing reagent, the pellet in each of fourseparate tubes was treated as follows: Eighty microliters of lysisbuffer (10 mM Tris HCl, pH 8.0, and 0.5% TWEEN 20) was added, followedby 10 μL of the thermostable protease Pre-Taq, (1 U/μL, BoehringerMannheim Biochemicals, Indianapolis, Ind.), and the tubes were heated at100° C. for 5 min. After heat treatment, 10 μL of 250 mM NaOH was added,and the tubes were again heated at 105° C. for 10 min, followed bycentrifugation at 14,000 rpm for 2 min.

Method of Invention—No Use of Lysing Reagent

Samples not contacted with lysis reagent were treated as follows: thepellet from each of four separate tubes was resuspended in 100 μL ofPBS.

Samples prepared using both above-methods were processed identically:the tubes were centrifuged at 14,000 rpm for 2 min, the supernatantfluid from each tube was carefully decanted into new tubes and stored atroom temperature prior to analysis. DNA content for each tube wasanalyzed using the TaqMan β-actin assay and an ABI Prism 7700 SequenceDetector as described above, with calibration based on DNA standardspurchased from Perkin Elmer. The results are summarized in Table IV.

TABLE IV COMPARISON OF DNA RELEASED FROM WHITE BLOOD CELLS WITH ANDWITHOUT TREATMENT WITH LYSIS REAGENT # Cell Treatment DNA ng/μl Average1 control 2.2 2.93 2 control 3.0 3 control 3.6 4 control 2.4 5 invention0.006 0.01 6 invention 0.016 7 invention 0.011 8 invention 0.007

These data indicate that in the presence of lysis reagent, there isapproximately a 300-fold greater amount of DNA released from the whiteblood cells. Since DNA released from white blood cells is not expectedto harbor mutations, deletions or other specific cancer markerscirculating in blood from a primary tumor, such non-target related DNAincreases non-specific background, and therefore, has a deleteriouseffect on an assay for either free circulating DNA in body fluids basedon the detection of specific alterations in DNA associated with cancer.

Example 3 Comparison of Invention with Qiagen Kit Method for ExtractingDNA from Serum

The following example demonstrates a comparison of the commercial Qiagenkit and the method of the present invention for extracting DNA from thesame serum pool.

For the isolation of DNA from serum or plasma based on the method of theinvention, all initial steps were performed on ice to minimize possibledegradation of DNA by serum nucleases. ACES buffer(N-(2-acetamido)-2-aminoethanesulfonic acid) from Sigma Chemical Co.,St. Louis, Mo. was prepared as a 250 mM stock solution, pH 6.8. DNAcapture polymer, poly(1-vinylimidazolehydrochloride-co-2-hydroxyethylmethacrylate) at a 76:24 monomer weightratio and at 2.4% solids, was synthesized by protocols described in U.S.Pat. No. 5,582,988. It is a random linear vinyl addition co-polymer madeusing conventional solution co-polymerization in N,N-dimethylformamidewith an azo initiator. The copolymer (or simply polymer) was mixed withan excess of water and concentrated HCl was added until a clear solutionwas obtained. The solution was then diafiltered.

Two hundred microliters of serum or plasma were added to a 1.5 mLmicrofuge-tube followed by the addition of 100 uL of the ACES bufferstock. After mixing by means of a vortex mixer, 15 uL of the aqueouscapture polymer solution was added to the tube and the sample was againmixed for 5 sec. using a vortex mixer. The tube was centrifuged by meansof a Eppendorf Microcentrifuge model 5415 (Brinkman Instruments,Westbury, N.Y.) at maximum speed for 2 min, and the supernatant fluidwas decanted. One hundred microliters of 20 mM NaOH was added to thetube containing the pellet, and the tube was mixed by means of a Vortexmixer, followed by heating at 100° C. for 5 min. Samples were eithermaintained at 4° C. and assayed immediately following extraction orstored frozen prior to use.

For comparison, DNA was also extracted from serum or plasma using aQIAmp Blood Kit (cat 29104) from Qiagen Corp., Chatsworth, Calif.according to the manufacturer's recommended procedure. Buffers AL, AWand AE were provided in the kit. Two hundred microliters of serum werecombined with 200 uL of 0.05M potassium phosphate buffer, pH 7.5, and200 uL of Buffer AL and 25 uL of Proteinase K solution (lysing reagent)provided in the kit and the contents were immediately mixed for 15seconds using a vortex mixer. Following incubation at 70° C. for 10 min,210 uL of ethanol was added, and the sample was again mixed using thevortex mixer. DNA was extracted by means of a QIAamp spin column into a2 mL collection tube. After applying the sample, the tube wascentrifuged at 6,000×g for 1 min. The tube containing the filtrate wasdiscarded. Five hundred microliters of Buffer AW was added, and thecolumn was again centrifuged for 1 min, and the tube containing thefiltrate was discarded. The column was washed an additional time withbuffer AW and DNA was then eluted from the column with 200 uL of BufferAE or distilled water preheated to 70° C. After addition of the bufferor water, the tube was incubated at room temperature for 1 min and thencentrifuged at 6,000×g for 1 min.

A comparison of the steps in the Quiagen kit method and the method ofthe present invention are shown in Table V. The Quiagen kit requires atleast 8 steps as compared with the method of the invention, whichrequires 3 steps.

TABLE V COMPARISON OF STEPS INVOLVED IN DNA EXTRACTION USING THE METHODOF THE INVENTION AND QIAGEN METHOD IzMn(76/24) Polymer Capture QIAGENKit 1 ACES Buffer addition 1 PBS buffer addition 2 Polymer addition 2QIAGEN Protease Treatment 3 DNA release by NaOH 3 Incubation at 70° C.for 10 min. 4 Ethanol addition 5 Load QIAamp spin column and spin 6Buffer wash the column, 1 min spin 7 Buffer wash the column, 3 min spin8 Buffer elute the column

A comparison of amplifiable β-actin DNA as measured by the TaqManβ-actin protocol (8 replicates) is shown in Table VI and indicates a 58%improvement in recoverable amplifiable DNA using the method of theinvention (60.6 ng/mL serum) as compared to the Quiagen method (25.3ng/mL serum).

TABLE VI COMPARISON OF β-ACTIN DNA EXTRACTION USING THE METHOD OF THEINVENTION AND QIAGEN METHOD Serum ngDNA/ DNA Vol DNA ngDNA/μl ml Sample# Prep (μl) ng/μ AVEG SDTEV serum serum 1 Polymer 200 0.038 0.0606250.016475 0.0606 60.63 2 Polymer 200 0.06 3 Polymer 200 0.06 4 Polymer200 0.095 5 Polymer 200 0.051 6 Polymer 200 0.06 7 Polymer 200 0.068 8Polymer 200 0.053 1 QIAGEN 200 0.032 0.02525 0.014945 0.0253 25.25 2QIAGEN 200 0.013 3 QIAGEN 200 0.022 4 QIAGEN 200 0.025 5 QIAGEN 2000.059 6 QIAGEN 200 0.016 7 QIAGEN 200 0.015 8 QIAGEN 200 0.02

Example 4 Recovery of β-Actin DNA from Serum of Individuals Diagnosedwith Pancreatic Cancer and Controls Using the Method of the Invention

This example provides the results of experiments providing aquantitative measure of the amount of β-Actin DNA recovered from theserum of normal and pancreatic cancer patients using the method of theinvention in accordance with the materials and procedures of Example 8herein. β-Actin DNA so recovered from each sample was quantified usingthe TaqMan β-actin protocol described earlier.

As shown in Table VII, using the method of the invention a total of 8replicates from the same human serum pool yielded an average of 12 ng ofβ-Actin DNA/mL of serum, whereas β-Actin DNA in the serum of 10different pancreatic cancer patients recovered using the method of theinvention was greatly elevated (average=146 ng/mL). These findings ofelevated β-Actin DNA in the serum of individuals having pancreaticcancer as compared with that of normals are supported by several reportsin the literature (4,9).

TABLE VII β-ACTIN DNA EXTRACTION FROM NORMAL SERUM POOL AND SERUM FROMINDIVIDUALS AFFLICTED WITH PANCREATIC CANCER USING THE METHOD OF THEINVENTION ngDNA/ Sample source Quantity ngDNA/μl ml Sample # 300 μlng/μl AVEG SDTEV in serum in serum 1 Human Serum 0.045 0.072875 0.0494530.0121 12 2 Pool 0.056 3 0.19 4 0.056 5 0.072 6 0.032 7 0.078 8 0.054 1Pancreatic 1 0.881875 1.07686 0.1470 146 2 Cancer Patient 0.33 3 Serum0.16 4 0.88 5 0.69 6 0.075 7 0.32 8 0.43 9 3.4 10 1.1

Example 5 Comparison of the Method of the Invention and Qiagen Methodfor Recovery of β-Actin DNA from Serum of Individuals Diagnosed withPancreatic Cancer

In this example, β-Actin DNA recovery from 6 patients with confirmedpancreatic cancer was compared using the method of the invention and theQiagen method in accordance with the materials and procedures of Example3 herein. In general, as shown in Table VIII, the method of theinvention yielded either higher or comparable levels of β-Actin DNA asassayed by the TaqMan β-Actin assay. Depending upon the sample,measurable DNA concentrations ranged from 31 to 310 ng/mL.

TABLE VIII COMPARISON OF β-ACTIN DNA EXTRACTION FROM SERUM OFINDIVIDUALS AFFLICTED WITH PANCREATIC CANCER USING THE METHOD OF THEINVENTION AND QIAGEN METHOD Sample # Method ng DNA/mL serum 1 Qiagen 2631 Polymer Capture 260 2 Qiagen 95 2 Polymer Capture 102 3 Qiagen 88 3Polymer Capture 235 4 Qiagen 310 4 Polymer Capture 275 5 Qiagen 31 5Polymer Capture 38 6 Qiagen 57 6 Polymer Capture 65Results are the average of 4 replicates per sample, except for sample 1and 2 which are the average of 6 replicates. Sample 2 evaluated with theQiagen protocol is the average of 2 replicates.

Example 6 Isolation of Circulating DNA from Serum of Normal and CancerPatients Using the Method of the Invention

This example illustrates the utility of the method of the invention forisolating circulating DNA from serum of 20 normals and 30 individualshaving a confirmed cancer diagnosis. Cancer patient sera included 10confirmed pancreatic cancer patients, and 20 colon cancer samples (8Dukes B, 5 Dukes C, and 7 Dukes D). The DNA was isolated according tothe method of the invention as in the procedure described in Example 2herein. DNA was quantified using the TaqMan β-actin assay. Polymercapture without use of a lysing reagent enabled circulating DNA to beconcentrated with minimal or no contamination with DNA from undesirablecell lysis and removal of PCR interferences that may be present inserum. DNA in each serum was quantified by means of the TaqMan assay forthe β-actin gene using the standard curve shown herein in FIG. 1.

The results of analyses for free circulating DNA in each sample areshown in Tables IX A and IX B and indicate that DNA levels are elevatedin serum from cancer patients compared with the serum from normalindividuals.

TABLE IX A DNA CONTENT IN THE SERUM OF CANCER PATIENTS Average # D.Ssupport # Diagnosis DNA ng/μl ng/ml ng/ml 1 139980708 Pancreatic 0.03517.5 26.4 2 310980084 Pancreatic 0.024 12 3 310980107 Pancreatic 0.02 104 310980130 Pancreatic 0.017 8.5 5 310980153 Pancreatic 0.029 14.5 6310980176 Pancreatic 0.037 18.5 7 1111980333 Pancreatic 0.22 110 82510980006 Pancreatic 0.043 21.5 9 2510980012 Pancreatic 0.054 27 102510980017 Pancreatic 0.049 24.5 11 139980709 Dukes B 0.17 85 135.5 121110980326 Dukes B 0.14 70 13 1110980328 Dukes B 0.1 50 14 1110980332Dukes B 0.11 55 15 2410980054 Dukes B 0.03 15 16 2410980059 Dukes B0.048 24 17 2611980009 Dukes B 1.4 700 18 2611980018 Dukes B 0.17 85 19139980701 Dukes C 0.011 5.5 100.13 20 1110980312 Dukes C 0.21 105 211110980319 Dukes C 0.39 195 22 1110980324 Dukes C 0.19 95 23 2411980086Dukes C N.D. N.D. 24 310980121 Dukes D 0.05 25 66.08 25 310980144 DukesD 0.055 27.5 26 310980190 Dukes D 0.051 25.5 27 2411980074 Dukes D 0.05728.5 28 2611980003 Dukes D 0.093 46.5 29 2611980004 Dukes D 0.05 25 302611980012 Dukes D 0.61 305

TABLE IX B DNA CONTENT IN SERUM OF NORMALS DNA # Unit # ng/2 μl ng/ml  1M58234 ND* ND  2 M58088 ND ND  3 M58089 0.0510 6.38  4 M58090 ND ND  5M58091 ND ND  6 M58092 0.0300 3.75  7 M58093 ND ND  8 M58094 0.0190 2.38 9* M58095 0.0360 4.50 10 M58111 0.0400 5.00 11 M58112 0.0370 4.63 12M58113 ND ND 13 M58115 0.0310 3.88 14 M58116 ND ND 15 M58118 0.0230 2.8816 M58120 0.1200 15.00  17 M58121 0.0390 4.88 18 M58124 0.0190 2.38 19M58126 0.0590 7.38  20* M58128 0.0290 3.63 *ND = below detection limit

Example 7 Detection of K-ras Mutations in the Serum of Pancreatic CancerPatients

In this example, an embodiment of the invention involving polymercapture of DNA from the serum of pancreatic cancer patients wasemployed. Restriction endonuclease mediated selective PCR (REMS PCR)wasperformed (Roberts, N. J. et al., 1999, BioTechniques 27:(3)418-422,Ward, R. et al., 1998, Am. J. Pathol. 153(2):373-379, and WO96/32500)followed by gel analysis was used to detect the presence of a K-rasmutation at codon 12 (K12-ras).

Serum or plasma (300 uL) from each of 3 pancreatic cancer patients wasadded to separate microfuge tubes, followed by addition of 100 uL of 250mM ACES (N-(2-Acetamido)-2-aminoethanesulfonic acid) buffer (pH 6.8 at23° C.). Fifteen microliters (15 uL) of polymer poly(1-vinylimidazole-co-2-hydroxyethyl methycrylate (weight ratio 77/23)was added (see U.S. Pat. Nos. 5,434,270; 5,523,368. and 5,582,988) andthe tubes were mixed by means of a Mini Vortexer (VWR Scientific,Rochester, N.Y.) for 10 seconds. The tubes were then centrifuged in anEppendorf Microcentrifuge, Model 5415, at maximum speed for 2 min. Thesupernatant fluid was decanted and 100 uL of 20 mM sodium hydroxide wasadded to each tube, and the pellet was resuspended by mixing and heatedto 100° C. for 10 min.

Each PCR admixture contained three sets of primers. The diagnosticprimers induce a Bstnl restriction site in wild-type ras, but not in amutation at ras codon 12. Thus, ras wild-type DNA is selectively cleavedduring PCR thermocycling, and mutant sequences of ras at codon 12 areenriched. The PCR control primer pair is used to confirm that PCRamplifiable DNA has been extracted, and the enzyme control primer pairconfirms that the restriction enzyme functioned during thermocycling.Reaction admixtures contained 12 units/100RL of recombinant Taqpolymerase, and a 5-fold excess by weight (0.842FLL) of Taq inhibitingantibody TP4-9.2 (see U.S. 15 U.S. Pat. Nos. 5,338,671 and 5,587,287)over the polymerase, 1 mM HT50 buffer (100 mM sodium chloride, and 50 mMTris (tris(hydroxymethyl)amino methane), pH 8.3, 0.3ELM of diagnosticprimers (see below), 5K15S (SEQ ID: NO 1) and 5K37 (SEQ ID: NO 2), 0.05pM of PCR control primer pairs, 3K42 (SEQ ID: NO 3) and 5BK5 (SEQ ID: NO4), 0.1˜LM of enzyme control primer pairs, 5N 12A (SEQ ID: NO 5) and3N13A (SEQ ID: NO 6), 0.2 mM total dinucleoside triphosphates (dNTPs),0.3 units/˜LL of Bsll (New England BioLabs, Beverly Mass.), 1 mmdithiothreitol (DTT), 5 mM magnesium chloride, sample (typically 3˜tL)and deionized water up to a final volume of 100 gL. The Taq polymeraseand anti-Taq antibodies were combined and incubated for 10-15 minutesprior to the addition of the other PCR components. Thermocyclingparameters were as follows: 1 cycle at 94° C. for 100 sec., and 36cycles at 92° C. for 15 sec, and 60° C. for 60 sec. The primer sequencesare as follows:

1. A kit for detection of K-ras mutation in a biological sample, said kit comprising a diagnostic K-ras primer selected from the group consisting of: <SEQ ID: NO 1> (a) TGAATATAAA CTTGTGGTAC CTGGAGC T (5K15S), <SEQ ID: NO 2> (b) ATATAAACTT GTGGTAGTTC CAGCTGGT (5K37), <SEQ ID: NO 3> (c) GAATTAGCTG TATCGTCAAG GCACTC (3K42), <SEQ ID: NO 4> (d) TCAGCAAAGA CAAGACAGGT A (5BK5), <SEQ ID: NO 5> (e) TATAGATGGT GAAACCTGTT TGTTGG (5N12A), <SEQ ID: NO 6> (f) CTTGCTATTA TTGATGGCAA CCACACAGA (3N13A)

(g) any combination of the foregoing.
 2. The oligonucleotide TGAATATAAA CTTGTGGTAC CTGGAGC T <SEQ ID: NO 1>.
 3. The oligonucleotide ATATAAACTT GTGGTAGTTC CAGCTGGT <SEQ ID: NO 2>.
 4. The oligonucleotide GAATTAGCTG TATCGTCAAG GCACTC <SEQ ID: NO 3>.
 5. The oligonucleotide TCAGCAAAGA CAAGACAGGT A <SEQ ID: NO 4>.
 6. The oligonucleotide TATAGATGGT GAAACCTGTT TGTTGG <SEQ ID: NO 5>.
 7. The oligonucleotide CTTGCTATTA TTGATGGCAA CCACACAGA <SEQ ID: NO 6>.
 8. A K-ras diagnostic primer comprising the oligonucleotide TGAATATAAA CTTGTGGTAC CTGGAGC T<SEQ ID: NO 1>.
 9. A K-ras diagnostic primer comprising the oligonucleotide ATATAAACTT GTGGTAGTTC CAGCTGGT <SEQ ID: NO 2>.
 10. A K-ras diagnostic primer comprising the oligonucleotide GAATTAGCTG TATCGTCAAG GCACTC <SEQ ID: NO 3>.
 11. A K-ras diagnostic primer comprising the oligonucleotide TCAGCAAAGA CAAGACAGGT A <SEQ ID: NO 4>.
 12. A K-ras diagnostic primer comprising the oligonucleotide TATAGATGGT GAAACCTGTT TGTTGG <SEQ ID: NO 5>.
 13. A K-ras diagnostic primer comprising the oligonucleotide CTTGCTATTA TTGATGGCAA CCACACAGA <SEQ ID: NO 6>. 